Pandora's Tower tells a haunting tale about a cursed young woman's slow transformation into a hideous beast, and the lengths to which the man she loves will go in order to save her. Aeron must brave the Thirteen Towers, which are suspended in the middle of a valley by chains connected to surrounding cliffs, and use his magical Oraclos Chain weapon to retrieve “master flesh,” the flesh of the giant monsters that reside within each tower, which he must feed to Elena in order to reverse her transformation. Aeron's interactions with Elena during their time together have a direct impact on the story, as the strength of their bond will determine which of the multiple endings is achieved.